diff --git a/External/pubchem_shape/PubChemShape.cpp b/External/pubchem_shape/PubChemShape.cpp
index 014fa3676..e25b44c18 100644
--- a/External/pubchem_shape/PubChemShape.cpp
+++ b/External/pubchem_shape/PubChemShape.cpp
@@ -283,15 +283,16 @@ ShapeInput PrepareConformer(const ROMol &mol, int confId, bool useColors) {
   res.shift = {-ave.x, -ave.y, -ave.z};
   res.coord.resize(nAlignmentAtoms * 3);
 
-  for (unsigned i = 0; i < nAtoms; ++i) {
+  for (unsigned i = 0, j = 0; i < nAtoms; ++i) {
     // use only non-H for alignment
     if (mol.getAtomWithIdx(i)->getAtomicNum() > 1) {
       RDGeom::Point3D pos = conformer.getAtomPos(i);
       pos -= ave;
 
-      res.coord[i * 3] = pos.x;
-      res.coord[(i * 3) + 1] = pos.y;
-      res.coord[(i * 3) + 2] = pos.z;
+      res.coord[j * 3] = pos.x;
+      res.coord[(j * 3) + 1] = pos.y;
+      res.coord[(j * 3) + 2] = pos.z;
+      ++j;
     }
   }
 
diff --git a/External/pubchem_shape/PubChemShape.hpp b/External/pubchem_shape/PubChemShape.hpp
index 245dba9d0..a55064f9d 100644
--- a/External/pubchem_shape/PubChemShape.hpp
+++ b/External/pubchem_shape/PubChemShape.hpp
@@ -2,6 +2,9 @@
 #include <map>
 #include <vector>
 
+#ifndef RDKIT_PUBCHEMSHAPE_GUARD
+#define RDKIT_PUBCHEMSHAPE_GUARD
+
 //! The input for the pubchem shape alignment code
 struct RDKIT_PUBCHEMSHAPE_EXPORT ShapeInput {
   std::vector<float> coord;
@@ -66,3 +69,5 @@ RDKIT_PUBCHEMSHAPE_EXPORT std::pair<double, double> AlignMolecule(
     int refConfId = -1, int fitConfId = -1, bool useColors = true,
     double opt_param = 1.0, unsigned int max_preiters = 10u,
     unsigned int max_postiters = 30u);
+
+#endif
\ No newline at end of file
diff --git a/External/pubchem_shape/test.cpp b/External/pubchem_shape/test.cpp
index 9dd34e290..737b09415 100644
--- a/External/pubchem_shape/test.cpp
+++ b/External/pubchem_shape/test.cpp
@@ -278,7 +278,7 @@ TEST_CASE("Github #8096") {
     REQUIRE(m2);
     std::vector<float> matrix(12, 0.0);
     auto [nbr_st, nbr_ct] = AlignMolecule(*m1, *m2, matrix);
-    CHECK_THAT(nbr_st, Catch::Matchers::WithinAbs(0.940, 0.005));
-    CHECK_THAT(nbr_ct, Catch::Matchers::WithinAbs(0.902, 0.005));
+    CHECK_THAT(nbr_st, Catch::Matchers::WithinAbs(1.0, 0.005));
+    CHECK_THAT(nbr_ct, Catch::Matchers::WithinAbs(1.0, 0.005));
   }
 }